Coarse-Graining of Molecular Liquids in Time and Space

俄勒冈大学的玛丽娜·古扎获得了化学系化学理论、模型和计算方法项目颁发的奖项。古恩扎博士开发了研究复杂分子液体的计算和理论方法。这种计算机模拟很有用，因为它们可以解释基于液体分子性质的实验结果。然而，他们在可研究的系统大小方面存在严重限制。为了能够模拟更大的系统，古萨和他的同事采用了一种粗粒化--粗粒化的积分方程式理论。这种方法在描述分子时只使用了必要的细节，从而减少了计算时间。这使得研究更大更复杂的系统成为可能。该方法已被证明在其结构、热力学和动力学性质的预测中非常准确。进一步优化该方法，将其扩展到许多系统，并使想要使用该方法的科学家能够使用该方法，是该项目的主要目标。该项目的第二个方面侧重于进一步开发一种研究蛋白质、核酸及其复合体的方法。古扎和她的研究小组开展了面向俄勒冈州农村学区的高中生的外联活动。这项研究的重点是扩大复杂分子液体模拟的长度尺度和时间尺度的范围。在第一个项目中，古萨和他的同事们正在扩展粗粒化积分方程论(IECG)方法的能力，以处理非均匀分子液体，例如，在固体界面上。在第二个项目中，他们致力于将朗之万蛋白质动力学方程(LE4PD)扩展到处理蛋白质、核酸及其复合体。该方法基于溶液中大分子动力学的朗之万方程，该方程还解释了大分子中局部构象势垒和内部疏水区的存在。通过与马尔可夫状态模型的集成来发展描述长时间跨越障碍的动力学的理论是这项工作的关键组成部分。

Marina Guenza of the University of Oregon is supported by an award from the Chemical Theory, Models and Computational Methods program in the Division of Chemistry. Dr. Guenza develops computational and theoretical methods to study complex molecular liquid. Such computer simulations are useful because they can explain experimental findings based on the molecular nature of the liquid. However, they have severe limitations in the size of the system that they can study. To allow simulation of larger systems, Guenza and coworkers employ a kind of coarse graining, the Integral Equation theory of Coarse-Graining (IECG). This approach uses only essential details in the description of the molecules thereby reducing computational time. This allows for the study of large and more complex systems. The method has been shown to be very accurate in its predictions of structural, thermodynamic, and dynamical properties. Further optimization of the method, its extension to many systems, and making the method accessible to the scientists that want to use it, are the main goals of this project. A second aspect of the project focuses on the further development of an approach to study proteins, nuclear acids and their complexes. Guenza and her research group engage in outreach activities to high school students from rural Oregon school districts. The focus of this research is to extend the range of length scales and time scales where complex molecular liquids can be simulated. In the first project, Guenza and coworkers are extending the capabilities of the Integral Equation theory of Coarse-Graining (IECG) approach to treat non-uniform molecular liquids, for example, at solid interfaces. In the second project, they are working to extend the Langevin Equation for Protein Dynamics (LE4PD) to treat proteins, nucleic acids, and their complexes. The approach is based on a Langevin equation for the dynamics of macromolecules in solution, which also accounts for the presence of local conformational barriers and the internal hydrophobic region in the macromolecule. Developing the theory to describe the long-time barrier-crossing dynamics by integration with Markov State Models is a key component of this work.